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No Access Submitted: 14 November 2019 Accepted: 18 February 2020 Published Online: 25 March 2020

  • Detection of single analyte and environmental samples with silicon nitride nanopores: Antarctic dirt particulates and DNA in artificial seawater
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Review of Scientific Instruments 91, 031301 (2020); https://doi.org/10.1063/1.5138210
David J. Niedzwiecki1,a), Yung-Chien Chou2, Zehui Xia1, Federico Thei3, and Marija Drndić2,a)
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  • David J. Niedzwiecki
  • Yung-Chien Chou
  • Zehui Xia
  • Federico Thei
  • Marija Drndić
ABSTRACT
Nanopore sensing is a powerful tool for the detection of biomolecules. Solid-state nanopores act as single-molecule sensors that can function in harsh conditions. Their resilient nature makes them attractive candidates for taking this technology into the field to measure environmental samples for life detection in space and water quality monitoring. Here, we discuss the fabrication of silicon nitride pores from ∼1.6 to 20 nm in diameter in 20-nm-thick silicon nitride membranes suspended on glass chips and their performance. We detect pure laboratory samples containing a single analyte including DNA, BSA, microRNA, TAT, and poly-D-lys-hydrobromide. We also measured an environmental (mixed-analyte) sample, containing Antarctic dirt provided by NASA Ames. For DNA measurements, in addition to using KCl and NaCl solutions, we used the artificial (synthetic) seawater, which is a mixture of different salts mimicking the composition of natural seawater. These samples were spiked with double-stranded DNA (dsDNA) fragments at different concentrations to establish the limits of nanopore sensitivity in candidate environment conditions. Nanopore chips were cleaned and reused for successive measurements. A stand-alone, 1-MHz-bandwidth Chimera amplifier was used to determine the DNA concentration in artificial seawater that we can detect in a practical time scale of a few minutes. We also designed and developed a new compact nanopore reader, a portable read-out device with miniaturized fluidic cells, which can obtain translocation data at bandwidths up to 100 kHz. Using this new instrument, we record translocations of 400 bp, 1000 bp, and 15000 bp dsDNA fragments and show discrimination by analysis of current amplitude and event duration histograms.

ACKNOWLEDGMENTS

The glass chips and nanopores were fabricated at the Pennovation Center and at the University of Pennsylvania’s Singh Center for Nanotechnology and at Rutgers University by Goeppert LLC. We thank Dr. Chris McKay from NASA Ames for providing samples of the Linnaeus Terrace dirt from Antarctic Dry Valleys. We also thank Jacob Swett at the University of Oxford for useful discussions and Michele Rossi, previously at Elements, SRL, for help with the portable nanopore reader. The nanopore reader and fluidic cell were developed here in collaboration with Elements, SRL, Italy. The work was supported by NASA SBIR Phase I No. S.11-3492 (2018-1) “Detecting life in ocean worlds with low-capacitance solid-state nanopores.” This work was carried out in part at the Singh Center for Nanotechnology, which is supported by the NSF National Nanotechnology Coordinated Infrastructure Program under Grant No. NNCI-1542153.

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